Variant report

Variant	rs7953477
Chromosome Location	chr12:59508265-59508266
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59507135..59508358-chr12:59543262..59544671,18	MCF-7	breast:
2	chr12:59506961..59508922-chr12:59510527..59512982,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1023797	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172909	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12367511	0.90[EUR][1000 genomes]
rs1500033	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1500034	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17628272	0.90[EUR][1000 genomes]
rs1846623	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1846624	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36082506	0.83[EUR][1000 genomes]
rs6581231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581232	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136863	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952875	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957634	0.88[EUR][1000 genomes]
rs908394	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv469412	chr12:59504600-59542117	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv559051	chr12:59504600-59542117	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59497200-59513400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:59501200-59513200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:59506000-59517400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:59506200-59509400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:59507800-59508400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:59507800-59508400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:59507800-59508400	Enhancers	Fetal Intestine Small	intestine
8	chr12:59507800-59508400	Enhancers	Fetal Stomach	stomach
9	chr12:59507800-59508600	Enhancers	Colon Smooth Muscle	Colon
10	chr12:59507800-59508800	Enhancers	Fetal Intestine Large	intestine
11	chr12:59507800-59509400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:59507800-59509800	Enhancers	NHDF-Ad	bronchial
13	chr12:59507800-59510000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:59507800-59510000	Enhancers	HUVEC	blood vessel
15	chr12:59507800-59510200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:59508200-59508400	Enhancers	HepG2	liver
17	chr12:59508200-59508600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:59508200-59508600	Enhancers	Brain Hippocampus Middle	brain
19	chr12:59508200-59509200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:59508200-59513200	Weak transcription	Esophagus	oesophagus
21	chr12:59508200-59513400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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